v2.0.0

CHANGES IN VERSION 2.0.0

NEW FEATURES

• Better integration with Bioconductor API:
  • Added BiocParallel support for all parallel functions.
  • Propagate mcols() from GRanges, remove hard-coded column names, and
    limit use of data.frame objects.
  • Drop functionality such as readBed() and writeWiggle() already present
    in the rtracklayer package maintained by the Bioconductor core team.
• polymeraseWave() is more reliable and has faster processing from several
  changes:
  • Parallel processing.
  • Less memory usage.
  • HMM calculations 10x faster not including parallel processing.
  • Genes are ignored if they have no reads within or nearby instead of
    blindly processing all annotated genes.
  • Errors from failure to fit distributions, etc are returned to the user
    via BiocParallel error handler bptry().

SIGNIFICANT USER-VISIBLE CHANGES

• Remove functions:
  • readBed() and writeWiggle() reimplement rtracklayer import.bed(), and
    export.bw() / export.wig().
  • tlsDeming(), tlsLoess(), and tlsSvd() total least squares fit functions,
    commented as unreliable by the author and not used anywhere in the code
    base.
  • Redundant runMetaGene-like functions metaGeneMatrix() and metaGene_nL().
  • averagePlot() does not have a sufficiently broad use case.
• Remove function arguments:
  • Broken NonMap/UnMAQ argument of polymeraseWave() and pausingIndex().
  • Buggy resampling arguments of getTxDensity().
  • Debug parameters from many functions. For troubleshooting faults, it is
    much more informative to use debugonce(), browser(), etc per
    adv-r.had.co.nz and improve the now included unit tests.
• Verbose flag now works for C functions. The large volume of C messages
  can be silenced as originally intended instead of always being verbose.
• Replace sweave package vignette with Rmd for easier user interaction.
  Less effort should be needed to maintain the vignette due to simpler
  syntax, and fewer obtuse LaTeX errors.
• Disable default plotting of getTxDensity(). Only functions whose names
  start with 'plot' automatically generate plots.
• getTxDensity() is faster and returns exact values instead of trapezoidal
  approximation.
• windowAnalysis() now has no upper limit on stepSize.
• polymeraseWave() returns GRanges instead of relative wave positions.
• polymeraseWave() has a new within argument to find waves beyond annotated
  gene boundaries.

BUG FIXES AND IMPROVEMENTS

• Fix windowAnalysis() "subscript out of bounds" error, and add corner case
  of empty ranges. Fix regression of only returning single chromosome.
• Fix corner cases of breakTranscriptsOnGenes() and combineTranscripts()
  failing when no break or join errors are detected.
• Fix breakTranscriptsOnGenes() failing to validate assumption that
  annotations do not overlap (GitHub issue #2).
• Fix polymeraseWave processing genes beyond chromosome boundaries and raise
  error when HMM fails to converge.
• Fix makeConsensusAnnotations not correctly validating presence of gene ID
  column. Additionally the gene ID column no longer uses the "gene_id"
  magic string and is configurable via the column argument.
• One can now control makeConsensusAnnotations() parallelism. Remove the
  hard coded 10 CPU cores.
• Move all packages from Depends to Imports to fix Travis-CI bootstrap
  errors.
• Add unit test suite using testthat:
  • All bugs discovered since version 1.7.0 now have corresponding
    regression tests.
  • Add lintr in unit tests to preserve code style.
• New maintainer in response to dead upstream.
• Add contributor instructions in README.
• Add GitHub continuous integration using Travis-CI, covr, and codecov.
• Fix R check errors, warnings and notes:
  • Fix RgammaMLE() namespace collision between R and C functions by
    renaming C function to Rgamma().
  • Add useDynamicSymbols removed by a previous maintainer in Bioconductor
    3.0.
• Fix BiocCheck errors, warnings and notes:
  • Drop use of <<- from writeWriggle()
  • Indent at multiples of 4 spaces.
  • Wrap lines at 80 columns.